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  • C12N2750/14141—Use of virus, viral particle or viral elements as a vector
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  • C12N2800/24—Vectors characterised by the absence of particular element, e.g. selectable marker, viral origin of replication

Definitions

• the present invention relates to methods of delivering exogenous, particularly heterologous, DNA sequences to a target, particularly a target cell, tissue, organ or organism.
• the invention relates to novel naked adeno-associated virus (AAV) vectors devoid of viral capsid proteins (hereinafter "AAVO") for the delivery to targets of heterologous DNA sequences.
• AAV adeno-associated virus
• Recombinant AAVO vectors of the invention may be used for in vitro, ex vivo, or in vivo delivery of an exogenous DNA sequence to a target.
• the invention also provides for methods of producing and purifying AAVO vectors.
• Gene therapy aims to correct defective genes that underlie the development of diseases.
• a common approach to addressing this issue involves the delivery of a normal gene to the nucleus. This gene may then be inserted into the genome of the targeted cell or may remain episomal. Delivery of a corrective gene to a subject's target cells can be carried out via numerous methods, including the use of viral vectors.
• viral vectors e.g, retrovirus, lentivirus, adenovirus, and the like
• AAV adeno-associated virus
• Adeno-associated virus is a member of the parvoviridae family.
• the AAV genome is composed of a linear single-stranded DNA molecule which contains approximately 4.7 kilobases (kb) and consists of two major open reading frames encoding the non- structural Rep (replication) and structural Cap (capsid) proteins. Flanking the AAV coding regions are two cis-acting nucleotide inverted terminal repeat (ITR) sequences, approximately 145 nucleotides in length, with interrupted palindromic sequences that can fold into hairpin structures that function as primers during initiation of DNA replication.
• ITR inverted terminal repeat
• ITR sequences In addition to their role in DNA replication, the ITR sequences have been shown to be necessary for viral integration, rescue from the host genome, and encapsidation of viral nucleic acid into mature virions (Muzyczka, (1992) Curr. Top. Micro. Immunol. 158:97-129).
• Vectors derived from AAV are particularly attractive for delivering genetic material because (i) they are able to infect (transduce) a wide variety of non-dividing and dividing cell types including muscle fibers and neurons; (ii) they are devoid of the virus structural genes, thereby eliminating the natural host cell responses to virus infection, e.g., interferon-mediated responses; (iii) wild-type viruses have never been associated with any pathology in humans; (iv) in contrast to wild type AAVs, which are capable of integrating into the host cell genome, replication-deficient AAV vectors generally persist as episomes, thus limiting the risk of insertional mutagenesis or activation of oncogenes; and (v) in contrast to other vector systems, AAV vectors do not trigger a significant immune response (see ii), thus granting long-term expression of the therapeutic transgenes (provided their gene products are not rejected).
• AAV vectors can also be produced at high titer and intra-arterial, intra-venous, or intra-peritoneal injections allow gene transfer to significant muscle regions through a single injection, at least in rodents (Goyenvalle et al, 2004; Fougerousse et al., 2007; Koppanati et al, 2010; Wang et al, 2009).
• AAV vectors also have multiple advantages over plasmid DNA with respect to delivering genetic material. For instance, expression of heterologous genes from plasmids is short-term, plasmids are usually of greater size, and plasmids need to be physically manipulated in order to be delivered into cells (e.g., microinjection, transfection, electroporation). Furthermore, plasmid transfer of genes such as dystrophin elicits an immune response in the host and is associated with low efficiency (Romero et al, 2004).
• AAV vectors may elicit a mild host immune response likely mediated by the viral capsid or processing impurities.
• use of immunosuppressants to control the immune response is only a temporary measure, as once a subject is taken off these immunosuppressants, the immune response returns (Lorain et al, 2008).
• AAV vector packaging capacity such as trans-splicing (ts) and overlapping (ov) AAV vector systems designed to deliver large therapeutic genes to target cells.
• ts trans-splicing
• ov overlapping
• AAV vector packaging capacity such as trans-splicing (ts) and overlapping (ov) AAV vector systems designed to deliver large therapeutic genes to target cells.
• lostal et al. bypassed the size limitation with respect to dysferlin cDNA, which cannot be directly incorporated into an AAV vector for gene transfer into muscle, by splitting the dysferlin cDNA at the exon 28/29 junction and cloning it into two independent AAV vectors carrying appropriate splice sequences (Lostal et al., 2010).
• the small packaging capacity remains a major limitation in AAV gene therapy. Removal of the capsid has not been considered a way by which the packaging capacity could be overcome because the capsid is considered essential to permit vector entry into the cell.
• AAV-mediated gene expression is relatively slow, given that single-stranded AAV DNA must be converted to double-stranded DNA prior to heterologous gene expression. While attempts have been made to circumvent this issue by constructing double-stranded DNA vectors, this strategy further limits the size of the transgene expression cassette that can be integrated into the AAV vector (McCarty, 2008; Varenika et al, 2009; Foust et al., 2009). Furthermore, effective AAV-mediated gene therapy in a growing organ can lose its effect due to episomal DNA dilution in dividing cells (Cunningham et al., 2009).
• the present invention addresses some or all of the aforementioned drawbacks associated with AAV vectors by providing recombinant AAVO ("rAAVO") vectors for in vitro, ex vivo, or in vivo delivery of exogenous DNA sequences to a cell, tissue, organ, or subject.
• rAAVO recombinant AAVO
• the present invention is based on the finding that exogenous DNA sequences can be incorporated into AAV genomes (or vectors) devoid of capsids (i.e., AAVO) and delivered into target cells, tissues, organs, or subjects for efficient expression of a protein or ribonucleotide (RNA) or desoxyribonucleotide (DNA) of interest without mediation of the uptake process by a viral capsid.
• capsid Prior to the present invention, the capsid was considered necessary for the efficient uptake of the viral vector into the cell and there would have been a reluctance to dispense with it.
• methods for purifying AAV vectors were largely based on antibodies against the capsid which would leave nonencapsidated DNA behind or on use of DNAase that would have degraded any nonencapsidated DNA.
• Structural features distinguishing the rAAVO vectors of the present invention from plasmid- based expression vectors include the lack of original (i.e. not inserted) bacterial DNA in rAAVO vectors, rAAVO vectors lack a prokaryotic origin of replication, rAAVO vectors are self-containing, i.e., they do not require any sequences other than the two ITRs, including the Rep binding and terminal resolution sites (RBS and TRS), and an exogenous sequence between the ITRs, the presence of ITR sequences that form hairpins, the fact that rAAVO vectors are of eukaryotic origin (i.e., they are produced in eukaryotic cells) and the absence of bacterial-type DNA methylation or indeed any other methylation considered abnormal by a mammalian host.
• rAAVO vectors In general, it is preferred for the present vectors not to contain any prokaryotic DNA but it is contemplated that some prokaryotic DNA may be inserted as an exogenous sequence.
• Another important feature distinguishing rAAVO vectors from plasmid expression vectors is that rAAVO vectors consist in both single-stand or double-strand linear DNA, while plasmids are always double-stranded DNA.
• Some of the advantages of rAAVO vectors of the present invention over plasmid-based expression vectors include, but are not limited to: 1) plasmids contain bacterial DNA sequences and are subjected to prokary otic-specific methylation, i.e.
• rAAVO vector sequences are of eukaryotic origin; 2) while plasmids require the presence of a resistance gene during the production process, rAAVO vectors do not; 3) while a circular plasmid is not delivered to the nucleus upon introduction into a cell and requires overloading to bypass degradation by cellular nucleases, rAAVO vectors contain viral cis- elements, i.e., ITRs, that confer resistance to nucleases and can be designed to be targeted and delivered to the nucleus.
• ITRs viral cis- elements
• rAAVO vectors over conventional AAV vectors include, but are not limited to: 1) conventional AAV vectors have capsids that elicit a host immune response, whereas such a response is not triggered by capsid-less rAAVO vectors; 2) conventional AAV vectors have limited cargo capacity (approximately 4.5 kb), whereas rAAVO vectors are not subject to this limit, i.e., they can incorporate sequences from very short ones to more than 10% longer than the cargo capacity of the wild-type AAV genome , i.e.
• preparations of conventional AAV vectors are inhomogeneous (i.e., contain mixtures of complete AAV vectors and empty capsids), whereas rAAVO vectors are substantially homogeneous in nature; and 4) the composition of conventional AAV vectors is heterogeneous even after purification, whereas rAAVO vectors can be characterized fully using standard DNA analytical techniques allowing one to obtain a homogenous and completely characterized end product. Furthermore, given the lack of immunogenicity of rAAVO vectors, mixtures of different rAAVO vectors can be co-administered to a cell, organ, or subject, either through identical or different routes.
• the invention provides rAAVO vectors and their use for expressing proteins or RNA or DNA in, for example, cells, organs, tissues, and subjects.
• Such expression is not limited to one protein or RNA molecule, but can involve the expression of multiple proteins and/or RNAs via multiple distinct rAAVO vectors delivered into the host.
• Such transduction can be transient or permanent.
• rAAVO vectors that encode a product intended to elicit a permanent modification or correction of the host genome e.g., via a meganuclease or zinc finger nuclease
• rAAVO vectors can deliver coding or non-coding DNA that can influence gene editing, such as exon skipping.
• rAAVO vectors of the invention can also be employed for vaccination by delivering a rAAVO vector encoding a protein or a protein/DNA mixture by intramuscular injection followed by a second injection, preferably intramuscular, both injections conveying the expression of the same antigen (protein) which is not recognized by the immune repertoire of the host (self).
• rAAVO vectors of the invention have utility for transgene delivery into embryonic stem cells (ESCs) or ovary cells for the generation of genetic knock- out or knock-in animal models.
• ESCs embryonic stem cells
• ovary cells for the generation of genetic knock- out or knock-in animal models.
• rAAVO vectors of the invention can also be used to induce immune tolerance to a gene product by application in the neonatal period in order to pave the way for subsequent immune-tolerance for a substitutive therapy such as an enzyme therapy (Sun, B, et al Am. J. Hum. Genet. 2007;81 : 1042-1049).
• a substitutive therapy such as an enzyme therapy
• Balb/c mice are sensitive and mount both cellular and humoral immune responses to GFP. By injecting them with a small amount of rAAVO carrying GFP gene at birth, tolerance can be induced such that subsequent injections of larger amounts of rAAVO or other GFP carrying vector will not elicit significant immune responses.
• the invention provides an isolated linear nucleic acid molecule comprising in this order: a first adeno-associated virus (AAV) inverted terminal repeat (ITR), a nucleotide sequence of interest (for example an expression cassette of an exogenous DNA) and a second AAV ITR, wherein said nucleic acid molecule is devoid of AAV capsid protein coding sequences.
• AAV adeno-associated virus
• ITR inverted terminal repeat
• nucleic acid molecule of the invention is devoid of viral capsid protein coding sequences (i.e. it is devoid of AAV capsid genes but also of capsid genes of other viruses).
• the nucleic acid molecule is also devoid of AAV Rep protein coding sequences. Accordingly, in a preferred embodiment, the nucleic acid molecule of the invention is devoid of functional AAV cap and AAV rep genes.
• the invention provides for a minimal rAAVO vector which has two AAV inverted terminal repeats (ITRs) and a nucleotide sequence of interest (for example an expression cassette), each of said ITRs having an interrupted (or noncontiguous) palindromic sequence, i.e., a sequence composed of three segments: a first segment and a last segment that are identical when read 5' ⁇ 3' but hybridize when placed against each other, and a segment that is different that separates the identical segments.
• Such sequences, notably the ITRs form hairpin structures.
• the nucleotide sequence of interest can in particular be an expression cassette comprising at least one promoter operatively linked to an exogenous DNA sequence, and flanked on each end by one ITR.
• the rAAVO vector does not encode capsid proteins, and the rAAVO vector is not encapsidated.
• the rAAVO vector can be single- stranded, double- stranded, or duplex with one or both ends covalently linked via the ITR palindrome. In a preferred embodiment, the rAAVO vector is single- stranded.
• the exogenous DNA sequence encodes a therapeutic protein, such as dystrophin; LARGE (Barresi et al, 2004); dysferlin; calpain 3; Dux 4; LAMA2; ⁇ -, ⁇ -, ⁇ -, and ⁇ -sarcoglycan; FKRP, fukutin, WASP, factor VIII, factor IX, SMN1, U7, modified U7 (U.S.
• the exogenous DNA sequences encode antisense oligonucleotides ("AONs") or RNAs (coding or non-coding) such as siRNAs, shRNAs, micro-RNAs, and their antisense counterparts (e.g., antagoMiR).
• AONs antisense oligonucleotides
• RNAs coding or non-coding
• siRNAs e.g., siRNAs
• shRNAs e.g., a mutated gene that causes a detrimental phenotype when expressed
• the rAAVO vector comprises a template nucleotide sequence used as a correcting DNA strand to be inserted after a double-strand break provided by a meganuclease- or zinc finger nuclease.
• the rAAVO vector of the invention may contain other introduced sequences from extraviral origin as desired.
• a so-called suicide gene can be introduced to eliminate transduced cells.
• noninserted bacterial DNA is not present and preferably no bacterial DNA is present at all.
• the rAAVO vector of the invention can also be used in a method for the delivery of a nucleotide sequence of interest to a target cell.
• the method may in particular be a method for delivering a therapeutic gene of interest to a cell of a subject in need thereof.
• the invention allows for the in vivo expression of a polypeptide, protein, or oligonucleotide encoded by a therapeutic exogenous DNA sequence in cells in a subject such that therapeutic levels of the polypeptide, protein, or oligonucleotide are expressed.
• the invention relates to a method of delivering a selected gene into a cell, an organ, or tissue such as skeletal or cardiac muscle.
• the invention is not limited to the delivery and expression of a selected gene only in muscle cells, but is also applicable to other cell types in which expression of a therapeutic polypeptide, protein, or oligonucleotide is desired, for instance, neural cells.
• the invention relates to rAAVO vector-mediated delivery of a desired exogenous DNA sequence to neural cells by intracranial or intrathecal administration in vivo.
• delivery can be topical, intra-tissue (e.g., intramuscular, intracardiac, intrahepatic, intrarenal, intracerebral), conjunctival (e.g., extra-orbital, intraorbital, retroorbital, intraretinal, sub-retinal), mucosal (e.g., oral, rectal, nasal, pulmonary), intrathecal, intravesical, intracranial, systemic, intraperitoneal, subcutaneous, cutaneous, intravascular (e.g. intravenous, intraarterial), and intralymphatic.
• passive tissue transduction via high pressure intravascular infusion e.g. intravenous or intraarterial infusion, and intracellular injection, such as intranuclear microinjection or intracytoplasmic injection, are also contemplated.
• delivery is not limited to one species of rAAVO vector.
• multiple rAAVO vectors comprising different exogenous DNA sequences can be delivered simultaneously or sequentially to the target cell, tissue, organ, or subject. Therefore, this strategy can allow for the expression of multiple genes. Delivery can also be performed multiple times and, importantly for gene therapy in the clinical setting, in subsequent increasing or decreasing doses, given the lack of an anti-capsid host immune response due to the absence of a viral capsid. It is anticipated that no anti-capsid response will occur as there is no capsid. This can be confirmed, if desired, by multiple injections along the lines of Example 5 ( Figure 7) and by measurement of antibody response or of specific T cell activation or proliferation.
• the invention provides a method for making capsid-less rAAVO vectors, notably a method with a sufficiently high yield to provide sufficient vector for in vivo experiments.
• the method includes providing cells comprising two AAV ITRs, a nucleotide sequence of interest (e.g. an expression cassette comprising usually at least one promoter operatively linked to an exogenous DNA except for the delivery of a pure DNA template) positioned between the ITRs.
• the nucleotide sequence of interest is flanked on each end by one ITR and does not encode AAV capsid proteins, and the cells do not express AAV capsid proteins.
• the cells either already contain Rep or are transduced with a vector to contain Rep and are then grown under conditions permitting replication and release of DNA comprising the ITRs and the expression cassette and constituting the rAAVO vector.
• the rAAVO vector can then be collected and purified from the cells or supernatant as free released rAAVO vector or as exosomes or microparticles.
• the invention provides for host cell lines that have stably integrated a rAAVO genome into their own genome.
• the host cell line is an invertebrate cell line, preferably insect Sf9 cells.
• the host cell line is a mammalian cell line, preferably 293 cells.
• the Rep-encoding gene can be stably integrated into the host cell line (e.g., Sf9 cells).
• the means of introducing the Rep gene are multiple: e.g., transfection of plasmid, infection of a vector expressing Rep, stable cell lines expressing Rep.
• the mammalian host cell is isolated from a subject afflicted with a disease.
• the autologous host cell is preferably isolated from tissue that is directly affected by the disease and fails to express normal levels of a gene product, expresses a mutated and either nonfunctional or poorly functional gene product, or aberrantly overexpresses a gene product leading to the disease.
• the host cell is a stem cell.
• rAAVO transduction can result in, for example, the transient transduction of a given stem cell population where the transferred episomal gene or non-coding RNA is diluted upon subsequent cell passages.
• rAAVO-mediated transfer of an engineered meganuclease can lead to lasting genetic modification in stem cells (Silva et al, 2011).
• the meganuclease itself would be diluted upon subsequent cell divisions
• the rAAVO-meganuclease-mediated genetic modification will be inherited in a Mendelian manner through subsequent cell divisions. This could rectify a major drawback of meganuclease use.
• the invention provides for methods of purifying rAAVO vectors from host cell lines that have stably integrated a rAAVO genome into their own genome.
• the plasmid backbone is not suitable for rAAVO production given its prokaryotic origin, which carries a significant risk of immunogenicity.
• rAAVO production undergoes two steps: first, excision ("rescue") from the vector backbone via Rep proteins, and second, amplification of the excised vector genome by Rep proteins.
• rAAVO vectors are purified as DNA molecules.
• the rAAVO vectors are purified as exosomes or microparticles.
• the invention also provides for a method of treating a disease in a subject comprising introducing into a target cell in need thereof (in particular a muscle cell or tissue) of the subject a therapeutically effective amount of a rAAVO vector, optionally with a pharmaceutically acceptable carrier. While the rAAVO vector can be introduced in the presence of a carrier, such a carrier is not required.
• the rAAVO vector implemented comprises a nucleotide sequence of interest useful for treating the disease.
• the rAAVO vector may comprise a desired exogenous DNA sequence operably linked to control elements capable of directing transcription of the desired polypeptide, protein, or oligonucleotide encoded by the exogenous DNA sequence when introduced into the subject.
• the rAAVO vector can be administered via any suitable route as provided above, and elsewhere herein.
• the disease is Duchenne muscular dystrophy (DMD) and the transgene is dystrophin or a rAAVO encoding an optimized U7 harboring an appropriate antisense sequence allowing for the skipping of exon 23 in the mdx mouse model (see Goyenvalle et al., 2004).
• This rAAV0-U7 vector can be administered, for example, via intra-arterial injection of the femoral artery under parallel blockage of venous flow by a garrot proximal to the injection site. The resulting exon skipping and dystrophin restoration can be observed as soon as 4 weeks after administration to the transduced muscle tissue.
• the invention further provides for a method of treating a genetic or acquired muscle disease or disorder (or simply adding a gene or suppressing one) in a subject by (1) establishing a myoblast culture from a muscle biopsy of a subject with the disease (Bigot et al., 2008 ; Benchaouir et al., 2007), (2) delivering a rAAVO vector to myoblasts or to muscle tissue, the vector comprising the desired exogenous DNA sequence operably linked to control elements capable of directing transcription of the desired polypeptide, protein, or oligonucleotide encoded by the exogenous DNA sequence, (3) collecting exosomes or microparticles harboring the vector bearing the exogenous DNA sequence from the culture or collecting rAAVO vectors in the form of DNA, and (4) delivering the collected rAAVO-filled exosomes or microparticles or rAAVO vectors in the form of DNA into the subject.
• the exosomes or microparticles can have a particular tropism (e.g
• stem cells isolated from a patient can be transduced ex vivo to correct the deficiency caused by a mutation of a gene product in a host, or alternatively, to correct a genetic defect using a rAAVO-encoded DNA-cutting enzyme such as a zinc finger nuclease (Connelly et al., 2010).
• a rAAVO-encoded DNA-cutting enzyme such as a zinc finger nuclease (Connelly et al., 2010).
• the DNA-cutting enzyme is a meganuclease (Silva et al, 2011).
• the DNA-cutting enzyme is a TAL effector nuclease (Sun et al, 2012).
• Stem cells such as mesenchymal stem cells, hematopoietic stem cells, and iPS cells, are attractive targets for ex vivo modification with rAAVO vectors for potential cellular and gene therapy of inherited and acquired disorders.
• Certain advantages that make these cell types ideal for therapy include their ability to differentiate into multiple lineages, their ability to proliferate and self-renew, migrate to injury sites, and the fact that they are hypoimmunogenic when transduced ex vivo, allowing transplantation back into the host upon correction of the underlying defect (Li et al., 2009; Benchaouir et al., 2007).
• rAAVO vectors can bypass this shortcoming due to their non-dependence on the viral capsid for cell entry, particularly when combined with microparticle- or exosome-mediated delivery.
• AAV Ad.
• rAAVO vectors can bypass this shortcoming due to their non-dependence on the viral capsid for cell entry, particularly when combined with microparticle- or exosome-mediated delivery.
• the disease is DMD.
• a particularly interesting application will be the use of AAV0 in cancer therapy because of the ability to repeat the treatment until a tumor is reduced or eliminated, since no immune response is anticipated with the rAAVO vector of the invention.
• Figure 1 is a schematic comparison of conventional AAV (capsid-containing) and rAAVO. While conventional AAV vectors (top) have two components, capsid and genome, the rAAVO vectors (bottom) are capsid-less.
• Figure 2 is a scheme for rAAVO vector synthesis and downstream applications.
• Figure 2a shows a 5L bioreactor (B. Braun Medical Inc.), which can be used to amplify AAV0 in Sf9 cells, and an Akta Purifier 100 (B. Braun Medical Inc.), which can be used for downstream AAV0 purification processes.
• Figure 2b is a schematic detailing the AAV0 amplification process and downstream purification process using the Sf9 cell system.
• FIG. 3a is a schematic of the AAVO-GFP plasmid, which is based on the pFBGR plasmid and is used to make AAV0 in host cells.
• An ITR from AAV2 flanks both ends of the GFP expression cassette.
• the GFP expression cassette comprises, in the direction of transcription, a cytomegalovirus (CMV) promoter, a plO promoter, and a DNA sequence encoding GFP, and a transcriptional termination sequence.
• CMV cytomegalovirus
• plO plO promoter
• DNA sequence encoding GFP and a transcriptional termination sequence.
• a blasticidin S- resistance gene Outside the region sandwiched between and including the two ITRs is a blasticidin S- resistance gene, which is operably linked to the Orgyia pseudotsugata immediate early- 1 (Op IE-1) promoter.
• Figure 3b is a schematic representation of the general process of AAV genome amplification.
• the AAV genome is removed from the host genome and is amplified (Berns et al., 2007; Nash et al., 2007).
• Figure 4 is an agarose gel of undigested rAAVO vector or rAAVO vector digested with SnaBI enzyme.
• the bands on the agarose gel reflect the various conformations of rAAVO (depicted in the schematic on the right) after DNA recovery at the end of the production process.
• the bands in the first lane of the agarose gel are DNA size markers.
• the second lane, labeled "Ctrl” is DNA from undigested rAAVO. Bands corresponding to rAAVO concatemers are indicated.
• the letters "A" and "A"' reflect DNA products shown in the schematic on the right.
• the vast majority of rAAVO is in monomeric form (double-stranded or converted ⁇ 2.5kb).
• the bands in the third lane labeled "SnaBI”, are DNA from rAAVO digested with SnaBI enzyme.
• the letters “B” and “C” reflect DNA products shown in the schematic on the right. SnaBI digestion releases a 380 bp fragment containing the ITR (band “C”).
• Figure 5a is a fluorescence micrograph of 293 cells transfected with rAAVO-GFP vector using polyethylenimine (PEI) as a transfection reagent. 1 x 10 6 cells were transfected with 5 ⁇ g (left panel) and 9 ⁇ g (right panel) of rAAVO-GFP for 48 hours.
• Figure 5b is a fluorescence micrograph of C2C12 myoblasts microinjected with a solution (0.02 mg/ml) of AAV0-GFP vector either into nuclei (Upper panel) or into cytoplasm (Lower panel) by using a Xenoworks microinjection system (Sutter Instruments).
• Tetramethylrhodamine 70,000 MW lysine-fixable dextran was also co-microinjected as an area marker of microinjection. Two days after microinjections, myotubes were fixed using paraformaldehyde 3.7% (Sigma) and permeabilized with 0.5% triton before further fluorescent stainings. Left panels show nuclei stained by DAPI (Sigma). Middle panels show GFP florescence. Right panels show dextran staining allowing for the confirmation of the microinjection site (nucleus versus cytoplasm). Fluorescent images were acquired using a Nikon Ti microscope equipped with a CoolSNAP HQ2 camera (Roper Scientific), using a 40x 1.0 NA PL APO oil objective, driven by Metamorph (Molecular Devices).
• Figure 6a is a scheme of a mouse leg being injected intra-arterially with AAV0-GFP (100 ⁇ g of AAV0-GFP in 1 ml of PBS).
• Figure 6b is a fluorescence micrograph of a mouse leg that has been injected (two left panels) and one that has not been injected (two right panels); it shows that without intra-arterial injection of AAV0-GFP, no GFP signal is visible (right panels). Left panels show that intra-arterial injection of AAV0-GFP results in efficient expression of GFP in the leg after two weeks.
• Figure 6c shows GFP expression in cryosections of muscle tissue after intra-arterial injection of the leg (transversal (left panel) and longitudinal (right panel) 10 ⁇ muscle sections).
• Figure 7 is a fluorescence micrograph of mouse leg after two intra-arterial injections of AAVO-GFP in 1 week intervals. As shown in the scheme in the upper panel, the first injection was performed in the left leg (100 ⁇ g of AAVO-GFP in 1 ml of PBS), and the second in the right leg (100 ⁇ g of AAVO-GFP in 1 ml of PBS). Mice were allowed to recover for 8 weeks after the second injection prior to analysis. Fluorescence micrographs in the lower panel show that both legs were transduced with equal efficiency, suggesting that the first injection did not have a negative effect on the second injection.
• Figure 8 is an agarose gel (1%) of undigested rAAVO vector (encoding GFP under the CMV promoter) (300 ng middle lane, and 1,5 ⁇ g right lane).
• the bands on the agarose gel (2.6 kbase) reflect the linear monomeric single-stranded structure of rAAVO after DNA recovery at the end of the production process.
• the bands in the left lane of the agarose gel are DNA size markers.
• Figure 9 is an electron microscopy micrograph of AAVo in the presence of SSB (single strand binding protein). AAVo appears as a linear structure, which is single stranded as revealed by SSB embodiment.
• SSB single strand binding protein
• Figure 10 is a 4-12% gradient SDS-polyacrylamide gel showing protein contents in AAVo samples after purification by either a commercial DNA purification device (Qiagen Plasmid Plus Maxi kit, Qiagen AAVo) or our chromatography system (purified AAVo). Different amounts of AAVo encoding either GFP or U7 were loaded onto a 4-12% gradient SDS- polyacrylamide gel and separated by electrophoresis. Proteins were revealed by silver staining. Note that no protein contaminants could be detected after purification by using our chromatography procedure.
• the present invention provides an isolated linear nucleic acid molecule comprising in this order: a first adeno-associated virus (AAV) inverted terminal repeat (ITR), an expression cassette of an exogenous DNA and a second AAV ITR, wherein said nucleic acid molecule is devoid of AAV capsid protein coding sequences.
• AAV adeno-associated virus
• ITR inverted terminal repeat
• the nucleic acid molecule of the present invention is a rAAV vector devoid of capsid proteins (rAAVO), and may be used for the delivery of a desired exogenous DNA sequence for in vitro, ex vivo, or in vivo use of the same.
• compositions and methods of the invention are described in detail below. Although particular compositions and methods are exemplified herein, it is understood that any of a number of alternative compositions and methods are applicable and suitable for use in practicing the invention.
• AAVO refers to a capsid-less AAV vector construct containing the ITRs and any desired cargo, e.g., an exogenous gene or other polynucleotide and a promoter, but not the capsid.
• the capsid-less AAV vector construct does not contain sequences encoding the AAV Rep proteins.
• AAVO vector or "recombinant AAVO vector (“rAAVO”)” as used herein refers to a capsid-less AAV construct that comprises, as minimal components, two ITRs and an exogenous DNA sequence to be transferred to a host operably linked or not to control elements. There is no requirement that all ITRs originate from one type of AAV.
• the terms “AAVO vector”, “rAAVO vector” and “nucleic acid molecule of the invention” are herein used interchangeably.
• AAVO-plasmid refers to a circular double-stranded DNA that encodes the rAAVO vector, is capable of amplification in bacterial cells (i.e., has a selection marker allowing for growth of bacteria that have been transformed with the plasmid), and is introduced into a host cell for purposes of generating the rAAVO vector itself, which is either a linear single- or eventually double-stranded DNA.
• ITRs inverted terminal repeats
• AAV viral cis- elements named so because of their symmetry. These elements are essential for efficient multiplication of an AAV genome. It is hypothesized that the minimal defining elements indispensable for ITR function are a Rep-binding site (RBS; 5'-GCGCGCTCGCTCGCTC-3 ' for AAV2) and a terminal resolution site (TRS; 5'-AGTTGG-3' for AAV2) plus a variable palindromic sequence allowing for hairpin formation.
• an ITR comprises at least these three elements (RBS, TRS and sequences allowing the formation of an hairpin).
• ITR refers to ITRs of known natural AAV serotypes (e.g. ITR of a serotype 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or 11 AAV), to chimeric ITRs formed by the fusion of ITR elements derived from different serotypes, and to functional variant thereof.
• functional variant of an ITR it is referred to a sequence presenting a sequence identity of at least 80%, 85%, 90%, preferably of at least 95% with a known ITR, allowing multiplication of the sequence that includes said ITR in the presence of Rep proteins, and allowing the transduction of a cell without the need of a transfection aid (as shown in the examples).
• administering refers to delivery of a plasmid or vector of the invention for recombinant protein or nucleotide expression to a cell or to cells and/or tissues and/or organs of a subject. Such administering, introducing, or delivering may take place in vivo, in vitro, or ex vivo.
• a plasmid for recombinant protein or polypeptide expression may be introduced into a cell by transfection, which typically means insertion of heterologous DNA into a cell by chemical means (e.g., calcium phosphate transfection, polyethyleneimine (PEI), or lipofection); physical means (electroporation or microinjection); infection, which typically refers to introduction by way of an infectious agent, i.e., a virus (e.g., bacculovirus expressing AAV Rep genes); or transduction, which in microbiology refers to stable infection of a cell with a virus or the transfer of genetic material from one microorganism to another by way of a viral agent (e.g., a bacteriophage).
• transfection typically means insertion of heterologous DNA into a cell by chemical means (e.g., calcium phosphate transfection, polyethyleneimine (PEI), or lipofection); physical means (electroporation or microinjection); infection, which typically refers to introduction by way of an
• a vector according to the invention for recombinant polypeptide, protein, or oligonucleotide expression may be delivered by physical means (e.g., calcium phosphate transfection, electroporation, microinjection or lipofection), or by preparing the vector with a pharmaceutically acceptable carrier for in vitro, ex vivo, or in vivo delivery to a cell, tissue, organ, or a subject.
• physical means e.g., calcium phosphate transfection, electroporation, microinjection or lipofection
• a pharmaceutically acceptable carrier for in vitro, ex vivo, or in vivo delivery to a cell, tissue, organ, or a subject.
• an AAVO vector of the invention can enter cells without the aid of physical means or a carrier.
• oligonucleotide and “polynucleotide” usually refer to, respectively, generally smaller, nucleic acid fragments having from 4 to about 100 bases or generally larger (e.g., in excess of 100 bases and up to 30 kilobases) nucleic acid molecules and a sequence that is either complementary (antisense) or identical (sense) to the sequence of a messenger RNA (mRNA) or miRNA fragment or molecule.
• mRNA messenger RNA
• Oligonucleotides can also refer to DNA or RNA molecules that are either transcribed or non-transcribed.
• central nervous system or "CNS” as used herein refers to the art recognized use of the term.
• the CNS pertains to the brain, optic nerves, cranial nerves, and spinal cord.
• the CNS also comprises the cerebrospinal fluid, which fills the ventricles of the brain and the central canal of the spinal cord.
• Regions of the brain include, but are not limited to, the striatum, hippocampus, cortex, basal ganglia, subthalamic nucleus (STN), pedunculopontine nucleus (PPN), substantia nigra (SN), thalamus, putamen, or caudate regions of the brain, as well as the cerebellum, spinal cord or combinations thereof.
• catamerize or “concatemerize” as used herein refers to forming a polynucleotide molecule by linking sequences that repeat.
• control elements refers to DNA sequences that are capable of directing or regulating the transcription of the exogenous DNA sequence upon delivery into a cell, tissue, and/or organ of a subject.
• Converted double-strand form refers to the final rAAVO form which is operational in the host.
• exogenous DNA sequence refers to a nucleic acid sequence that does not originate from the host in which it is placed. It may be identical to the host's DNA or heterologous. An example is a sequence of interest inserted into a vector.
• exogenous DNA sequences may be derived from a variety of sources including DNA, cDNA, synthetic DNA, and RNA.
• exogenous DNA sequences may comprise genomic DNA which may or may not include introns either naturally occurring or artificial. Moreover, such genomic DNA may be obtained in association with promoter regions or poly A signal sequences.
• the exogenous DNA sequences in the present invention can be cDNA.
• exogenous DNA sequence includes without limitation any DNA sequence whose expression produces a gene product that is to be expressed in a host cell.
• the gene product may affect the physiology of the host cell.
• Exogenous DNA sequences also encompass DNA sequences that encode antisense oligonucleotides.
• exosome refers to a vesicle made from one or more cell membrane proteins. Vesicles are normally produced in the endocytic-lysosomal system of a cell and are then expelled, secreted or “shed” by the cell.
• microparticle refers to membrane-ensheathed cell fragments carrying specific protein and RNA cargo (See EP Application 10306226.1).
• expression cassette refers to an exogenous DNA sequence that is operably linked to a promoter or other regulatory sequence sufficient to direct transcription of the transgene.
• Suitable promoters include, for example, tissue specific promoters. Promoters can also be of AAV origin.
• gene delivery refers to methods or systems for reliably inserting foreign nucleic acid sequences, e.g., DNA, into host cells. Such methods can result in transient expression of non-integrated transferred DNA, extra-chromosomal replication and expression of transferred replicons (e.g., episomes), or integration of transferred genetic material into the genomic DNA of host cells. Gene transfer provides a unique approach for the treatment of acquired and inherited diseases.
• genetic muscle disorder refers to, but is not limited to, a neuromuscular or musculoskeletal disease or disorder, including without limitation, a neuromuscular disease caused by dominant mutation(s), recessive mutation(s), X-linked nuclear DNA mutation(s), or mitochondrial DNA mutation(s); also including large-range chromatin deletions which may or may not contain a gene but impacts gene editing. Examples include dominant or recessive limb girdle muscular dystrophies, Duchenne and Becker MD, Myotonic Dystrophy, Facioscapulohumeral dystrophy, and others.
• host cell refers to, for example microorganisms, yeast cells, insect cells, and mammalian cells, that can be, or have been, used as recipients of rAAV vectors.
• the term includes the progeny of the original cell which has been transduced.
• a "host cell” as used herein generally refers to a cell which has been transduced with an exogenous DNA sequence. It is understood that the progeny of a single parental cell may not necessarily be completely identical in morphology or in genomic or total DNA complement to the original parent, due to natural, accidental, or deliberate mutation.
• neural cells refers to cells that have been isolated from the brain, spinal cord or cells from any region of the central nervous system, as well as any cell present in the brain, spinal cord, or central nervous system of a subject.
• Examples of neural cells include neuronal cells, such as nerve cells that transmit nerve or chemical signals to and from the brain, such as sensory neurons or bipolar neurons that carry messages from the body's sense receptors (eyes, ears, etc.) to the CNS; motoneurons or multipolar neurons cells that carry signals from the muscles and glands to the CNS (e.g., spinal motor neurons, pyramidal neurons, Purkinje cells.); interneurons or pseudopolare cells which form the neural wiring within the CNS.
• neuronal cells such as nerve cells that transmit nerve or chemical signals to and from the brain, such as sensory neurons or bipolar neurons that carry messages from the body's sense receptors (eyes, ears, etc.) to the CNS
• motoneurons or multipolar neurons cells that carry signals from the muscles and glands to the CNS (e.g.,
• neural cells are also intended to include glial cells, which make up 90 percent of the brain's cells. Glial cells are nerve cells that do not carry nerve impulses. Types of glial cells include, but are not limited to, Schwann's cells, satellite cells, microglia, oligodendroglia, and astroglia.
• neurodegenerative disorder or "neurological disorder” as used herein refers to a disorder which causes morphological and/or functional abnormality of a neural cell or a population of neural cells.
• the neurodegenerative disorder can result in an impairment or absence of a normal neurological function or presence of an abnormal neurological function in a subject.
• neurodegenerative disorders can be the result of disease, injury, and/or aging.
• Non-limiting examples of morphological and functional abnormalities include physical deterioration and/or death of neural cells, abnormal growth patterns of neural cells, abnormalities in the physical connection between neural cells, under- or over production of a substance or substances, e.g., a neurotransmitter, by neural cells, failure of neural cells to produce a substance or substances which it normally produces, production of substances, e.g., neurotransmitters, and/or transmission of electrical impulses in abnormal patterns or at abnormal times.
• Neurodegeneration can occur in any area of the brain of a subject and is seen with many disorders including, for example, head trauma, stroke, ALS, multiple sclerosis, Huntington's disease, Parkinson's disease, and Alzheimer's disease.
• operably linked as used herein relative to the rAAVO vector means that nucleotide components of the rAAVO vector are functionally related to one another for operative control of a selected coding sequence.
• "operably linked" nucleic acid sequences are contiguous, and, in the case of a secretory leader, contiguous and in reading frame. However, enhancers do not have to be contiguous.
• rAAVO means including a genomic or other encoding sequence plus a control element (promoter), or a sense or anti sense oligonucleotide sequence between two ITR elements.
• the vector will have a control element, for example to drive transcription of U7 or RNAi or shRNA.
• rAAVO vectors can be used to deliver DNA that does not necessarily need to be transcribed and will thus lack the control element (e.g., a correcting matrix for zinc-finger or TAL exonuclease- or meganuclease-mediated gene repair).
• pharmaceutically acceptable refers to molecular entities and compositions that are physiologically tolerable and do not typically produce toxicity or an allergic or similar untoward reaction, such as gastric upset, dizziness and the like, when administered to a human.
• pharmaceutically acceptable means approved by a regulatory agency of the Federal or a state government or listed in the U.S. Pharmacopeia or other generally recognized pharmacopeia for use in animals, and more particularly in humans.
• polypeptide and protein are used interchangeably herein and refer to a polymer of amino acids and includes full-length proteins and fragments thereof.
• the invention also includes nucleic acids that encode those polypeptides having slight variations in amino acid sequences or other properties from a known amino acid sequence.
• Amino acid substitutions can be selected by known parameters to be neutral and can be introduced into the nucleic acid sequence encoding it by standard methods such as induced point, deletion, insertion and substitution mutants. Minor changes in amino acid sequence are generally preferred, such as conservative amino acid replacements, small internal deletions or insertions, and additions or deletions at the ends of the molecules. These modifications can result in changes in the amino acid sequence, provide silent mutations, modify a restriction site, or provide other specific mutations. Additionally, they can result in a beneficial change to the encoded protein.
• purified refers to material that has been isolated under conditions that reduce or eliminate the presence of unrelated materials, i.e. impurities, including native materials from which the material is obtained.
• purified rAAVO vector DNA is preferably substantially free of cell or culture components, including tissue culture components, contaminants, and the like. Exosomes or microparticles containing rAAVO can be purified using specialized cell sorter machines which select for particles as small as 80 or even 60 ⁇ . See EP 10306226.1.
• substantially free is used operationally, in the context of analytical testing of the material.
• purified material substantially free of impurities is at least 50% pure; more preferably, at least 90% pure, and more preferably still at least 99% pure. Purity can be evaluated by chromatography, gel electrophoresis, immunoassay, composition analysis, biological assay, and other methods known in the art.
• recombinant refers to nucleic acids, vectors, polypeptides, or proteins that have been generated using DNA recombination (cloning) methods and are distinguishable from native or wild-type nucleic acids, vectors, polypeptides, or proteins.
• rescue refers to release of the AAV0 genome from a duplex molecular form, e.g., either contained in a plasmid, heterologous virus genome (e.g., baculovirus), or a provirus in the cellular genome.
• the release and replication processes together are typically considered to comprise rescue.
• Several steps in the replication and release pathway were inferred from in vitro assays (Ward and Berns, 1991; Hong et al, 1992; Hong et al., 1994). Briefly, a recombination event occurs between the extruded duplex ITR resulting in a covalently closed-ended replication intermediate, previously referred to as "no- end" DNA (Ni et al., 1994).
• Either of the AAV p5 Rep proteins (Rep 78 or Rep 68) have sequence specific DNA binding and nicking activities and act on the closed-ended substrate.
• the Rep proteins bind to the stem region of the ITR and unwind the duplex DNA to expose the single strand nicking site, the terminal resolution site (trs).
• Either the Rep protein or cellular helicase activities unwind the ITR, thereby providing a 5'-overhang, ca.125 nt, and a free 3'-OH group that is extended by the cellular polymerase complex.
• a linear bimolecular duplex molecule is the product of terminal resolution events on either ends of the no-end intermediate.
• the bimolecular duplex DNA is now equivalent to annealed AAV genomes and replication may proceed indistinguishably for both rescued provirus DNA or virion-derived DNA.
• selectable marker refers to a gene, introduced into a cell, which confers a trait suitable for selection, so as to indicate the success of a transfection or other procedure meant to introduce exogenous DNA into a cell.
• anything that can be used as a detectable signal, either direct or indirect, is contemplated to be a selectable marker within the scope of the invention. Examples include, but are not limited to, a fluorescent marker such as GFP, a marker membrane peptide which allows for selection by cell sorting, and an antibiotic allowing for selection by resistance.
• Antibiotics and metabolic selectable markers are routinely used for generating stable eukaryotic cell lines.
• the antibiotic G418 is lethal to eukaryotic cells but is inactivated by the prokaryotic enzyme neomycin phospotransferase.
• hygromycin is toxic to mammalian cells, but is inactivated by hygromycin phosphotransferase.
• Chinese hamster ovary (CHO) cell lines have been developed lacking dihydrofolate reductase (DHFR). These cells are dependent on the exogenous glycine, hypoxanthine, and thymidine for survival. Accordingly, stable CHO cell lines can be generated by transfecting the desired transgene and DHFR in cis and culturing in HAT selective medium (reviewed in hacker and Wurn, 2007).
• subject includes, but is not limited to, humans, nonhuman primates such as chimpanzees and other apes and monkey species; farm animals such as cattle, sheep, pigs, goats and horses; domestic mammals such as dogs and cats; laboratory animals including rodents such as mice, rats and guinea pigs, and the like.
• farm animals such as cattle, sheep, pigs, goats and horses
• domestic mammals such as dogs and cats
• laboratory animals including rodents such as mice, rats and guinea pigs, and the like.
• rodents such as mice, rats and guinea pigs, and the like.
• the term does not denote a particular age or sex. Thus, adult and newborn subjects, as well as fetuses, whether male or female, are intended to be covered.
• therapeutic gene refers to a gene that, when expressed, confers a beneficial effect on the cell or tissue in which it is present, or on a mammal in which the gene is expressed.
• beneficial effects include amelioration of a sign or symptom of a condition or disease, prevention or inhibition of a condition or disease, or conferral of a desired characteristic.
• Therapeutic genes include genes that partially or wholly correct a genetic deficiency in a cell or mammal.
• therapeutically effective amount refers to an amount effective, at dosages and for periods of time necessary, to achieve the desired therapeutic result.
• a therapeutically effective amount of the recombinant vector may vary according to factors such as the disease state, age, sex, and weight of the individual and the ability of the vector to elicit a desired response in the individual.
• a therapeutically effective amount is also one in which any toxic or detrimental effect is outweighed by the therapeutically beneficial effects.
• tissue-specific promoter refers to a promoter that is operable in cells of a particular organ or tissue, such as the central nervous system (CNS).
• CNS central nervous system
• promoters for the CNS include but are not limited to, neuron-specific promoters (e.g., the neurofilament promoter; Byrne and Ruddle (1989) Proc. Natl. Acad. Sci. USA 86:5473-5477) and glial specific promoters (Morii et al. (1991) Biochem. Biophys Res. Commun. 175: 185-191).
• the promoter is tissue specific and is essentially not active outside the central nervous system, or the activity of the promoter is higher in the central nervous system that in other systems.
• promoters are the Chicken Beta Actin (CBA) promoter, neuron-specific enolase (NSE) promoter, creatine kinase promoter, desmin promoter, CAG promoter (composed of chicken b-actin promoter and CMV enhancer) (J. Miyazaki, 1989), liver-specific TBG promoter (2 copies of a-1 microglobulin/bikunin enhancer and thyroid hormone-binding globulin promoter) (Yang, 1997; Bell, 2011), CAG promoter (CMV enhancer/chicken ⁇ -actin promoter) coupled to TetOn/TetOff boxes (Lheriteau E, 2010), natural human U7 promoter (U.S.
• CBA Chicken Beta Actin
• NSE neuron-specific enolase
• CMV enhancer CMV enhancer
• TetOn/TetOff boxes Lheriteau E, 2010
• natural human U7 promoter U.S.
• promoter for cell-specific G protein-coupled receptor kinase 1 Khani SC, 2007
• Muscle cell specific promoters are also known (Himeda et al, 2011). Nonlimiting examples are muscle-specific creatine kinase promoter, desmin promoter (Li et al., 1993), myosin light chain promoters (Cox et al, 1992), chimeric muscle specific promoters (Frauli et al, 2003) and troponin C promoter-enhancer (cardiac muscle).
• transfection refers to the uptake of an exogenous nucleic acid molecule by a cell.
• a cell has been "transfected” when exogenous nucleic acid has been introduced inside the cell membrane.
• transfection techniques are generally known in the art. See, e.g., Graham et al. (1973) Virology, 52:456, Sambrook et al. (1989) Molecular Cloning, a laboratory manual, Cold Spring Harbor Laboratories, New York, Davis et al. (1986) Basic Methods in Molecular Biology, Elsevier, and Chu et al. (1981) Gene 13 : 197.
• Such techniques can be used to introduce one or more exogenous nucleic acid molecules into suitable host cells.
• vector refers to any non-plasmid genetic element, such as a virus, rAAVO, AAV, parvovirus, virion, and the like.
• ex vivo administration refers to a process where primary cells or an entire organ are harvested from a subject, a rAAVO vector is delivered into the cells, and the cells are readministered to the same or a different subject.
• any concentration range, percentage range, ratio range, or integer range is to be understood to include the value of any integer within the recited range and, when appropriate, fractions thereof (such as one tenth and one hundredth of an integer), unless otherwise indicated.
• any number range recited herein relating to any physical feature, such as polymer subunits, size or thickness are to be understood to include any integer within the recited range, unless otherwise indicated.
• the term “about” or “approximately” means within a statistically meaningful range of a value. Such a range can be within an order of magnitude, preferably within 50%, more preferably within 20%, more preferably still within 10%, and even more preferably within 5% of a given value or range. The allowable variation encompassed by the term “about” or “approximately” depends on the particular system under study, and can be readily appreciated by one of ordinary skill in the art.
• Viral capsids are in part responsible for the limited packaging capacity of AAV vectors.
• the lack of a capsid for the AAVO vector bypasses this limitation and allows for a desired exogenous DNA sequence, even one substantially exceeding the packaging capacity of AAV in size, to be incorporated into the AAVO vector and expressed upon introduction into a target cell, tissue, organ, or subject.
• inserts as large as 5, 8, 10 or 15 kb will be successfully transfected using the nucleic acid molecules (or rAAVO vectors) of the present invention.
• NCBI NC 002077; NC 001401; NC001729; NC001829; NC006152; NC 006260; NC 006261; Kotin and Smith, The Springer Index of Viruses,
• the AAVO backbone of the present invention can be derived from the genome of any AAV serotype.
• the AAV serotype is AAV2.
• AAV virus-mediated gene transfer involves the transfer of AAV viral particles encapsulated in AAV capsid proteins (e.g., Doenecke et al., 2010; Wang et al., 2011; Stieger et al., 2010; van der Marel S et al, 2011; Jiminez et al, 2011; White et al., 2011). While Doenecke et al reported plasmid AAV-mediated gene expression; this involved incorporating the AAV sequence into a bacterial plasmid.
• the plasmid backbone is not suitable for rAAVO production given its prokaryotic origin, which carries a significant risk of immunogenicity. Moreover, transfection of plasmids harboring AAVO will result in mainly rescued rAAVO, with no or poor amplification.).
• the present invention relates to an isolated capsid-free AAV genome comprising an expression cassette for an exogenous DNA but devoid of capsid coding sequences. This corresponds to an isolated linear nucleic acid molecule comprising in this order: a first AAV ITR, an expression cassette of an exogenous DNA and a second ITR.
• the nucleic acid molecule of the invention is a linear single- stranded or double-stranded nucleic acid.
• the nucleic acid molecule of the invention is single-stranded.
• the first ITR is located at the 5' end of the nucleic acid molecule.
• the second ITR is located at the 3' end of the nucleic acid molecule.
• the first ITR is located at the 5' end and the second ITR is located at the 3' end of the nucleic acid molecule.
• the isolated nucleic acid molecule backbone is derived from a known AAV genome such as one found in the above mentioned database.
• the isolated linear nucleic acid molecule of the invention may also be produced by genetic engineering by providing each element necessary for the construction of the vector, namely by providing two ITRs flanking an exogenous DNA expression cassette.
• the present invention relates to a vector which is a nucleic acid molecule that is linear. Accordingly, it should be understood that the present invention does not correspond to an AAV plasmid. Indeed, plasmids are circular nucleic acid molecule of bacterial origin. In the present case, therefore, the present invention and a plasmid differ both in term of structure of the subject-matter (in particular, linear versus circular) and also in view of the methods used for producing and purifying these different objects (see below), and also in view of their DNA methylation which is of prokaryotic type for plasmids and of eukaryotic type for rAAVO.
• the rAAVO vector (the nucleic acid molecule of the invention) differs from an AAV genome engineered into a different viral capsid such as that of a recombinant adenovirus (see for example WO 96/18727) because it is free of any viral capsid and has the capacity to be taken up into host cells directly without the interference of the host cell surface with a capsid protein, as well as to be transported from the cell cytoplasm into the nucleus without the interference of a capsid protein.
• the rAAVO vector described herein does not elicit the immune response in a host elicited by an adenoviral capsid or indeed any other viral capsid used to package the AAV genome.
• the AAVO backbone is derived from the AAV1, AAV2, AAV3, AAV4, AAV5, AAV6, AAV7, AAV8, AAV9, AAV10 or AAV11 genome.
• the AAVO backbone is derived from the AAV2 genome.
• the AAVO backbone is a synthetic backbone genetically engineered to include at its 5' and 3' ends ITRs derived from one or more of these AAV genomes.
• the two ITRs present in the nucleic acid molecule of the invention i.e in the rAAVO vector
• the two ITRs present in the nucleic acid molecule of the invention are the same, and can in particular be AAV2 ITRs.
• rAAVO plasmids i.e., plasmids used for later producing the rAAVO linear vector - see the definitions provided above
• rAAVO plasmids are constructed using known techniques to at least provide the following as operatively linked components in the direction of transcription: a 5' ITR; control elements including a promoter, an exogenous DNA sequence of interest; a transcriptional termination region; and a 3' ITR.
• the nucleotide sequences within the ITRs substantially replace the rep and cap coding regions.
• rep sequences are ideally encoded by a helper plasmid or vector, it can alternatively be carried by the rAAVO plasmid itself. In such cases, rep sequences are preferably located outside the region sandwiched between the ITRs, but can also be located within the region sandwiched between the ITRs.
• the desired exogenous DNA sequence is operably linked to control elements that direct the transcription or expression of an encoded polypeptide, protein, or oligonucleotide thereof in a cell, tissue, organ, or subject (i.e., in vitro, ex vivo, or in vivo).
• control elements can comprise control sequences normally associated with the selected gene.
• heterologous control sequences can be employed.
• Useful heterologous control sequences generally include those derived from sequences encoding mammalian or viral genes. Examples include, but are not limited to, promoters such as the SV40 early promoter; mouse mammary tumor virus LTR promoter; adenovirus major late promoter (Ad MLP); herpes simplex virus (HSV) promoters; a cytomegalovirus (CMV) promoter such as the CMV immediate early promoter region (CMVIE); a rous sarcoma virus (RSV) promoter; synthetic promoters; hybrid promoters; and the like.
• promoters such as the SV40 early promoter; mouse mammary tumor virus LTR promoter; adenovirus major late promoter (Ad MLP); herpes simplex virus (HSV) promoters; a cytomegalovirus (CMV) promoter such as the CMV immediate early promoter region (CMVIE); a rous sarcoma virus (RSV) promoter; synthetic promoters
• promoter sequences are commercially available from, e.g., Stratagene (San Diego, Calif). Alternatively, the promoter can be a tissue specific promoter. ITRs from any AAV serotype are suitable for use as 5' and 3' ITRs in the rAAVO plasmids of the present invention, and ITRs from different AAV serotypes can be used for each of the 5' and 3' ITRs. ITR sequences of many AAV serotypes are known. For example, SEQ ID NOs: 1 and 2 are the ITR sequences for AAV2. SEQ ID NOs: 3-6 provide the genome sequences for AAV1, 3, 4, and 5, respectively. ITR sequences for these serotypes are known in the art. See for example, Chiorini, JA et al, 1997, J. Virol.71(9): 6823-6833 Vol. 71, No. 9 which discloses ITR sequences for AAV2, AAV3 and AAV4.
• rAAVO plasmids can also include a selectable or selection marker for use in the establishment of a host cell rAAVO vector producing cell line.
• the selection marker is operably linked to a promoter, for example, the Orgyia pseudotsugata immediate early-1 promoter (Op IE-1).
• Op IE-1 Orgyia pseudotsugata immediate early-1 promoter
• the selection marker can be inserted downstream (i.e., 3') of the 3' ITR.
• the selection marker can be inserted upstream (i.e., 5') of the 5' ITR.
• Appropriate selection markers include, for example, those that confer drug resistance.
• Selection markers can be, for example, a blasticidin S-resistance gene, kanamycin, geneticin, and the like.
• the drug selection marker is a blasticidin S- resistance gene.
• Suitable exogenous DNA sequences for use in rAAVO plasmids and vectors are not limited in size due to the lack of a packaging constraint conferred by the viral capsid.
• the exogenous DNA sequence can exceed 5,000 bp, and in other embodiments, the exogenous DNA sequence can exceed 10,000 bp.
• an exogenous DNA sequence that exceeds the AAV packaging capacity by at least 10%, in fact by 20% and as large as 15 kb can be readily incorporated into AAV0 vectors.
• Exogenous DNA sequences include, for example, a gene that encodes a protein that is defective or missing from a recipient subject or a gene that encodes a protein having a desired biological or therapeutic effect (e.g., an antibacterial, antiviral or antitumor function).
• the exogenous DNA sequence will encode a gene product that can function to correct the expression of a defective gene or transcript (e.g., modified U7, meganuclease, transsplicing cassette, or to modulate post-transcriptional processing mechanisms (e.g., splicing)).
• the exogenous DNA sequence preferably encodes a protein that is relevant to the tissue to which it is administered.
• Exogenous DNA sequences can also encode corrective DNA strands, encode polypeptides, sense or antisense oligonucleotides, or RNAs (coding or non-coding; e.g., siRNAs, shRNAs, micro-RNAs, and their antisense counterparts (e.g., antagoMiR)).
• RNAs coding or non-coding; e.g., siRNAs, shRNAs, micro-RNAs, and their antisense counterparts (e.g., antagoMiR)).
• Suitable exogenous DNA sequences include, but are not limited to, those encoding for polypeptides, proteins, or oligonucleotides used for the treatment of endocrine, metabolic, hematologic, hepatic, cardiovascular, neurologic, musculoskeletal, urologic, pulmonary and immune disorders, including such disorders as inflammatory diseases, autoimmune, chronic, infectious, and genetic diseases, such as Duchenne muscular syndrome, Spinal muscular atrophy (SMA), AIDS, cancer (especially solid tumors), hypercholestemia, insulin disorders such as diabetes, growth disorders, various blood disorders including various anemias, thalassemias and hemophilia; genetic defects such as cystic fibrosis, Gaucher's Disease, Hurler's Disease, adenosine deaminase (ADA) deficiency, emphysema, Pompe disease, progeria, Parkinson's disease, Huntington disease, Alzheimer disease, ALS, epilepsy, stroke, and the like.
• Duchenne muscular syndrome Spinal
• Suitable transgenes to be encoded by the rAAVO vector include, for example, dystrophin; LARGE (Barresi et al., 2004); dysferlin; calpain 3; Dux 4; LAMA2; ⁇ -, ⁇ -, ⁇ -, and ⁇ - sarcoglycan; FKRP, fukutin, WASP, factor VIII, factor IX, SMN1, U7, Ul, RdCVF (Leveillard et al., 2010), a-glucosidase, LAMIN A/C, ZMPSTE 4, and actin.
• dystrophin LARGE (Barresi et al., 2004); dysferlin; calpain 3; Dux 4; LAMA2; ⁇ -, ⁇ -, ⁇ -, and ⁇ - sarcoglycan; FKRP, fukutin, WASP, factor VIII, factor IX, SMN1, U7, Ul, RdCVF (Leveillard
• any gene that encodes a protein or polypeptide that is either reduced or absent due to a mutation or which conveys a therapeutic benefit when overexpressed is considered to be within the scope of the invention.
• Also contemplated within the scope of the invention is the use of U7 technology to skip a gene out of frame (Pietri-Rouxel et al, 2010; U.S. Provisional Application 61/314,830 and WO2006/021724, herein incorporated by reference in their entirety. In this way, the expression of any gene can be regulated.
• the expression of genes in which the mutated version is known to be responsible for a disease, but not essential for the normal functioning of an organism or organ can be reduced via the U7 system.
• the U7 system can also be used for gene correction via trans-splicing (U.S. Provisional Patent Application No. 61/249,702 incorporated by reference in its entirety and EP2010/065142, which is also amenable for use with the rAAVO vector system.
• the rAAVO technology also allows for the parallel (i.e., decoupled) downregulation of a gene (e.g., a gene carrying a dominant mutation) and substitution of the same gene (to restore its physiological properties).
• one rAAVO vector is used to shut down a gene and another to introduce a normal copy of the same gene, reducing or eliminating interference of one with the other and permitting independent dosing of the two interventions.
• Such an approach can use e.g., out-of-frame exon skipping for gene silencing ⁇ Id.) using one rAAVO vector encoding an exon-skipping inducing AON and introduce a normal gene copy with a second rAAVO vector, wherein codon optimization renders the normal gene copy insensitive to the oligoanti sense sequence introducing the exon skipping ⁇ see, for example, Dominquez et al, 2010 and Millington-Ward et al, 2011).
• the two vectors can be dosed, and repeatedly, in an independent way, thereby allowing for adjustment of desired expression levels in the target tissue.
• different rAAVO vectors can be introduced in parallel to substitute, simultaneously or consecutively, different isoforms of a gene.
• the invention further provides a method for the production of a rAAVO vector, comprising:
• conditions allowing production of an AAV0 genome are particularly those comprising the induction of Rep protein expression, as is provided below.
• rAAVO vectors have been successfully isolated using plasmid purification kits appropriately scaled for the quantity of cells.
• the Qiagen EndoFree Plasmid kits have been used to isolate and purify rAAVO from Sf9 cells.
• Other methods developed for plasmid isolation may be adapted for rAAVO since the principle is the same, i.e., fractionating low molecular weight DNA from cellular genomic DNA, and removing protein and RNA from the product.
• Any cell line known in the art for producing AAV vectors can be used as a host rAAVO vector producing cell line.
• cell types e.g., Sf9, 293, and the like
• AAV-REP proteins can be used for AAV0 genome mobilization
• Other cell lines known to be infected by AAV can also be used, such as Huh-7, HeLa, HepG2, HeplA, 911, CHO, COS, MeWo, NIH3T3, A549, HT1180, monocytes, and mature and immature dendritic cells.
• Huh-7 Huh-7
• HeLa HeLa
• HepG2 HeplA
• 911 CHO
• COS COS
• MeWo NIH3T3T3T3T3
• A549 HT1180
• monocytes and mature and immature dendritic cells.
• rAAVO plasmids can be introduced into Sf9 cells by transient transfection using reagents (e.g., liposomal, calcium phosphate) or physical means (e.g., electroporation) known in the art.
• reagents e.g., liposomal, calcium phosphate
• physical means e.g., electroporation
• stable Sf9 cell lines which have stably integrated the rAAVO plasmids into their genomes can be established. Such stable cell lines can be established by incorporating a selection marker into the rAAVO plasmid as described above.
• AAV virions with capsids are produced by introducing a plasmid or plasmids encoding the rAAV genome, Rep proteins, and Cap proteins (Grimm et al, 1998). Upon introduction of these helper plasmids in trans, the AAV genome is "rescued" (i.e., released and subsequently recovered) from the host genome, and is further encapsidated to produce infectious AAV.
• helper plasmids Upon introduction of these helper plasmids in trans, the AAV genome is "rescued” (i.e., released and subsequently recovered) from the host genome, and is further encapsidated to produce infectious AAV.
• encapsidated AAV virus vectors were found to inefficiently transduce certain cell and tissue types.
• transductions with capsid-less AAVO vectors were unexpectedly found by the present inventors to be highly efficient for cell and tissues types that are difficult to transduce with conventional AAV virions.
• the present invention can be distinguished from such conventional methods in that only an AAV Rep encoding vector is required in trans.
• the AAV Rep encoding vector can be in the form of, for example, a bacculovirus expressing Rep proteins.
• Rep can be introduced by different means, e.g., via plasmid transfection, viral transduction, or stable integration in cell lines whereby expression is induced upon promoter activation.
• the rAAVO vector is rescued from the host genome, but is not further encapsidated into virion particles. It is also possible for the rAAVO plasmid to incorporate AAV Rep protein encoding nucleotide sequences.
• Rescued rAAVO vector can be purified in the form of DNA, using methods known in the art or using commercially available kits (e.g., Qiagen miniprep kit).
• Rescued rAAVO vector can also be purified in the form of exosomes, or microparticles. It is known in the art that many cell types release not only soluble proteins, but also complex protein/nucleic acid cargoes via membrane microvesicle shedding (Cocucci et al, 2009; EP 10306226.1). Such vesicles include microvesicles (also referred to as microparticles) and exosomes (also referred to as nanovesicles), both of which comprise proteins and RNA as cargo. Microvesicles are generated from the direct budding of the plasma membrane, and exosomes are released into the extracellular environment upon fusion of multivesicular endosomes with the plasma membrane.
• rAAVO vector-containing microvesicles and/or exosomes can be isolated from cells that have been transduced with the rAAVO vector.
• Microvesicles can be isolated by subjecting culture medium to filtration or ultracentrifugation at 20,000 g, and exosomes at 100,000 g. The optimal duration of ultracentrifugation can be experimentally-determined and will depend on the particular cell type from which the vesicles are isolated.
• the culture medium is first cleared by low-speed centrifugation (e.g., at 2000 g for 5-20 minutes) and subjected to spin concentration using, e.g., an Amicon spin column (Millipore, Watford, UK).
• Microvesicles and exosomes can be further purified via FACS or MACS by using specific antibodies that recognize specific surface antigens present on the microvesicles and exosomes.
• Other microvesicle and exosome purification methods include, but are not limited to, immunoprecipitation, affinity chromatography, filtration, and magnetic beads coated with specific antibodies or aptamers.
• vesicles are washed with, e.g., phosphate-buffered saline.
• One advantage of using microvesicles or exosomes to deliver rAAVO vesicles is that these vesicles can be targeted to various cell types by including on their membranes proteins recognized by specific receptors on the respective cell types. (See also EP 10306226.1)
• the host cell for rAAVO vector production is not limited to Sf9 cells.
• cells isolated from a subject afflicted with a disease can be used as hosts for rAAVO vector production.
• the cells can be isolated from tissue that is specifically affected by the disease. For example, muscle cells can be isolated from subjects suffering from muscular dystrophy.
• the rAAVO vector- transduced host cell e.g., cultured myoblasts
• the exosome and/or microparticle-containing culture supernatant can be used to deliver rAAVO vector into retinal cells to treat for example, RPGRTPl deficiency (Lheriteau et al, 2009) or retinitis pigmentosa (Ji-jing Pang et al, 2008).
• RPGRTPl deficiency Liheriteau et al, 2009
• retinitis pigmentosa Ji-jing Pang et al, 2008.
• the method for the production of a rAAVO vector comprises the steps of:
• Purification can in particular be implemented by submitting a cell pellet to an alkaline lysis, centrifuging the lysate and loading the supernatant on an ion exchange column (e.g. Sartobind Q) which retains nucleic acids.
• an ion exchange column e.g. Sartobind Q
• the material is then eluted (e.g. with a 1.2 M NaCl solution) and loaded on a gel filtration column (e.g. 6 fast flow GE).
• the AAV0 vector is then recovered by precipitation.
• rAAVO vectors can be used to transfect stem cells in vitro. These can be any kind of stem cell, e.g., embryonic stem cells, induced pluripotent stem cells, adult stem cells, and circulating or tissue-resident stem cells. Examples include, but are not limited to, CD 133+ cells, mesangioblasts, and ALDH+ stem cells. These stem cells can be cultivated ex vivo and transduced by rAAVO vectors to elicit transient or permanent modification of gene expression.
• stem cells can be cultivated ex vivo and transduced by rAAVO vectors to elicit transient or permanent modification of gene expression.
• Transient modification can be achieved by transduction of DNA or RNA sequences capable of inducing, silencing, or modifying gene expression either by introducing a gene coupled to a functional promoter or by introducing a Ul or U7 gene coupled to antisense-sequences capable of inducing an exon skipping event (in frame or out of frame) or by conferring trans-splicing sequences. If transduction is carried out during an early passage stage of cell culture, the rAAVO vector will be diluted through subsequent passages and eventually be lost, i.e., this will result in transient modification of gene expression.
• AAVO technology in this context is that due to the ability to incorporate sequences larger than that allowed by conventional AAV vectors as well as the possibility of transfection with one or multiple AAVO vectors containing complementary cargo, a correction DNA matrix can be simultaneously transferred into these cells.
• the cells to which the rAAVO vectors are delivered into can be derived from a human, and other mammals such as primates, horse, sheep, goat, pig, dog, rat, and mouse. rAAVO vectors can be delivered to any cell type, tissue, or organ without limitation. Examples of cells to which rAAVO can be delivered into include, but are not limited to, cells of the central nervous system (CNS), cells of the peripheral nervous system (PNS), muscle cells, osteoblasts, tumor cells, lymphocytes, and the like.
• CNS central nervous system
• PNS peripheral nervous system
• muscle cells muscle cells
• osteoblasts tumor cells
• lymphocytes lymphocytes
• tissues and organs to which rAAVO vectors can be delivered to include muscle, cardiac muscle, smooth muscle, brain, bone, connective tissue, heart, kidney, liver, lung, lymph node, mammary gland, myelin, prostate, testes, thymus, thyroid, trachea, and the like.
• Preferred cell types are muscle cells, cells of the CNS, and cells of the PNS.
• Preferred tissue and organs are muscle, heart, eye, and brain.
• tissue-specific expression of a DNA, RNA, polypeptide, protein, or AON of interest can be achieved by incorporating a tissue-specific promoter that drives the transcription of the exogenous DNA sequence in the rAAVO vector.
• tissue-specific promoters are as set forth previously.
• rAAVO vectors of the invention can be delivered to a cell by any means, including contacting the rAAVO vector with the cell. That is, rAAVO vectors do not absolutely require a transfection reagent for cell entry. This is a highly unexpected property since according to a classical hypothesis in this field, transduction by an AAV particle includes the endocytosis of the AAV particle, its intracellular trafficking to the nucleus and its nuclear import (see for example Ding et al., 2005). The encapsidated AAV genome is then released in the nucleus from the AAV particle.
• a capsid-less AAV genome is able to transduce a cell, and to reach the nucleus in a functional form from which gene expression could be achieved.
• the invention thus also relates to a method for the delivery of a nucleic acid of interest in a cell, comprising contacting at least one rAAVO vector with the cell's surface in the absence of a transfection agent or additional physical means to facilitate entry of said rAAVO vector into the cell. It also relates to a method for effecting the expression of a desired gene product or oligonucleotide in a cell comprising contacting at least one rAAVO vector with the cell's surface in the absence of a transfection agent or additional physical means to facilitate entry of said rAAVO vector into the cell.
• rAAVO vectors can present an alternative to transfection reagent-based delivery of genetic material into cells.
• rAAVO vectors can be used in conjunction with transfection reagents or physical means to facilitate entry into cells.
• the rAAVO vectors can be delivered into a cell by methods known in the art for delivering DNA into cells.
• rAAVO vectors can be introduced into cells by standard transfection methods (e.g., transfection reagents such as liposomes, alcohols, polylysine-rich compounds, arginine-rich compounds and calcium phosphate), microinjection, and the like.
• Other methods of introduction into cells include, for example, conjugation to proteins, nanoparticles, or packaging into cell-derived microvesicles (e.g., microparticles, exosomes) (See EP 10306226.1)
• rAAVO vectors can be incorporated into pharmaceutical compositions suitable for administration to a subject.
• the pharmaceutical composition comprises the rAAVO vectors and a pharmaceutically acceptable carrier.
• pharmaceutically acceptable carrier includes any and all solvents, dispersion media, coatings, antibacterial and antifungal agents, isotonic and absorption delaying agents, and the like that are physiologically compatible.
• pharmaceutically acceptable carriers include one or more of water, saline, phosphate buffered saline, dextrose, glycerol, ethanol and the like, as well as combinations thereof.
• compositions comprising rAAVO vectors can be delivered as, for example, ageratum, sprays, oral suspensions, suppositories, eye drops, and injectable suspensions.
• the rAAVO vectors of the invention can be incorporated into a pharmaceutical composition suitable for topical, systemic, intra-amniotic, intrathecal, intracranial, intraarterial, intravenous, intralymphatic, intraperitoneal, subcutaneous, tracheal, intra-tissue (e.g., intramuscular, intracardiac, intrahepatic, intrarenal, intracerebral), intrathecal, intravesical, conjunctival (e.g., extra-orbital, intraorbital, retroorbital, intraretinal), and mucosal (e.g., oral, rectal, nasal) administration.
• compositions for therapeutic purposes typically must be sterile and stable under the conditions of manufacture and storage.
• the composition can be formulated as a solution, microemulsion, dispersion, liposomes, or other ordered structure suitable to high rAAVO vector concentration.
• Sterile injectable solutions can be prepared by incorporating the rAAVO vector compound in the required amount in an appropriate buffer with one or a combination of ingredients enumerated above, as required, followed by filtered sterilization.
• rAAVO vectors For in vivo administration of rAAVO vectors, broad distribution of the rAAVO vectors can be achieved in muscle by, for example, intravenous, intra-arterial injection or hydrodynamic locoregional perfusion. Depending on dosage and mode of delivery, 20-95% of muscle fibres in a given target muscle can be transduced. Broad distribution of the rAAVO vectors can also be achieved in the CNS or PNS by injecting the rAAVO vector into the cerebrospinal fluid, e.g., by lumbar puncture (e.g., Kapadia et al., 1996).
• rAAVO vectors can be administered into specific sites of the brain to target a neural cell.
• stereotactic microinjection techniques Rost al., 2010
• Particularly preferred delivery methods are those that deliver the rAAVO vector to specific regions of the brain or muscle that require expression of a polypeptide, protein, or oligonucleotide encoded by the rAAVO vector.
• Direct injection of rAAVO vectors can take place using standard needle and syringe methodologies, or by needle-free technologies. The methods above can be performed with the rAAVO vectors in the form of pharmaceutical compositions comprising a pharmaceutically acceptable carrier or vehicle.
• Topical applications are also contemplated with or without cells, the latter using AAV0 directly on skin in a topical preparation for recessive forms of epidermolysis bullosa (see, e.g., Yan et al, 2010).
• Further methods for delivery of nucleic acid molecules are described, for example, in Boado et al., J. Pharm. Sci. 87: 1308-1315 (1998); Tyler et al, FEBS Lett. 421 :280-284 (1999); Pardridge et al, Proc. Natl Acad. Sci. USA 92:5592-5596 (1995); Boado, Adv. Drug Delivery Rev.
• Appropriate doses will depend on the particular cell type, tissue, organ, or subject being treated. When administered to a subject, dose will depend on the particular mammal being treated (e.g., human or nonhuman primate or other mammal), age and general condition of the subject to be treated, the severity of the condition being treated, the particular therapeutic polypeptide, protein, or oligonucleotide in question, its mode of administration, among other factors. An appropriate effective amount can be readily determined by one of skill in the art.
• a “therapeutically effective dose” will fall in a relatively broad range that can be determined through clinical trials and will depend on the particular application (neural cells will require very small amounts, while systemic injection would require large amounts).
• a therapeutically effective dose will be on the order of from about 1 ⁇ g to 100 g of the rAAVO vector. If exosomes or microparticles are used to deliver the rAAVO vector, then a therapeutically effective dose can be determined experimentally, but is expected to deliver from 1 ⁇ g to about 100 g of vector.
• an effective amount of rAAVO vector to be delivered to cells (1 x 10 6 cells) will be on the order of 1 to 20 ⁇ g rAAVO vector, preferably 5 to 15 ⁇ g, and more preferably 8 to 10 ⁇ g. Larger rAAV cargoes will require higher doses. If exosomes or microparticles are used, an effective in vitro dose can be determined experimentally but would be intended to deliver generally the same amount of vector.
• Treatment may involve administration of a single dose or multiple doses.
• Subject may be administered more than one dose, in fact multiple doses as needed, because the rAAVO vector does not elicit an anti-capsid host immune response due to the absence of a viral capsid.
• the number of doses administered can, for example, be on the order of 1-100, preferably 2-20 doses.
• rAAVO vectors of the invention are particularly suitable for delivering exogenous DNA sequences encoding polypeptides, proteins, or non-coding DNA, RNA, or oligonucleotides to, for example, cells of muscles and the CNS of subjects afflicted by a muscular or CNS disease.
• rAAVO vectors of the invention are particularly useful for a number of neurological and neurodegenerative diseases which can benefit from the expression of a peptide or protein which is defective in the diseases or disorder, such that expression of the peptide or protein would result in amelioration of symptoms associated with the disease or disorder.
• Some examples of applicable diseases include, but are not limited to, Duchenne muscular dystrophy, Spinal Muscular Atrophy, AIDS, Pompe disease, Parkinson's disease, Huntington disease, Alzheimer disease, Gaucher' s disease, Hurler's disease, adenosine deaminase (ADA) deficiency, emphysema, progeria, ALS, epilepsy, stroke, hypercholestemia, insulin disorders (e.g., diabetes), growth disorders, various blood disorders (e.g., anemias, thalassemias, hemophilia), genetic defects (e.g., cystic fibrosis), cancer (especially solid tumors), and the like.
• Duchenne muscular dystrophy Spinal Muscular Atrophy
• AIDS Pompe disease
• Parkinson's disease Huntington disease
• Alzheimer disease Gaucher' s disease
• Hurler's disease adenosine deaminase (ADA) deficiency
• emphysema progeria
• ALS epi
• rAAVO vectors can be used to correct the expression of an aberrant protein by targeting the underlying defective mechanism that gives rise to the aberrant protein responsible for the development of the disease.
• Aberrant splicing of the dystrophin gene can be corrected using rAAVO vectors containing, for example, nucleotide sequences that encode for AONs, U7, or a trans-splicing cassette ⁇ See, for example, Goyenvalle et al., 2004; Lorain et al., 2010; and the patent applications WO2006/021724, U.S. Provisional Application 61/314,830, U.S. Provisional Patent Application No. 61/249,702, and EP 2010/065142, all of which are herein incorporated by reference) to affected muscle tissue.
• a full-length dystrophin gene containing rAAVO vector can be delivered to affected muscle tissue.
• DMD Duchenne muscular dystrophy
• BMD Becker muscular dystrophy
• Efficacy of AAV0 vector-mediated therapy can be confirmed by introducing the rAAVO vectors expressing the transgene of interest into cells isolated from patients or animal models available in the art.
• DMD genetic animal models for DMD.
• the mdx mouse harbors a non-sense mutation in exon 23 of the dystrophin gene, which precludes the synthesis of full-length, wild-type dystrophin protein.
• the mdx mouse displays a compensatory mechanism counteracting the degeneration, which could maintain the regeneration process to restore the mechanical damage.
• the mdx mouse does not exhibit all symptoms of DMD and its life span is almost normal.
• the GRJVID (Golden Retriever Muscle Dystrophy) dog lacks functional dystrophin because of a splice site mutation in intron 6, which disrupts the reading frame.
• GRMD As with human DMD, the progressive degradation of fibers leads inexorably to skeletal musculature wasting with marked endomysial and perimysial fibrosis. Because of its DMD-like phenotype, GRJVID remains the best available model for the evaluation of potential therapies for DMD.
• Methods for delivering the rAAVO vectors of the invention are, in general, identical to those used for conventional viral vectors (See, for example, Goyenvalle et al, 2004; Toromanoff et al, 2010; Lowery et al., 2010; Duque et al., 2009). Even though deprived of capsid, AAV0 vectors do not need a transduction aid to enter the cell or the nucleus. Accordingly, the invention also provides a method for the delivery of an exogenous DNA in a cell, tissue or organ, comprising contacting said cell, tissue or organ with a rAAVO vector of the invention without use of a transduction aid.
• rAAVO vectors can be adopted to induce cell death by selective gene transfer in the context of cancer ⁇ See, for example, Gruber et al, 2011).
• the invention provides a method for the delivery of a nucleic acid of interest in a cell of a subject in need thereof, wherein the method is non-immunogenic or with reduced immunogenicity, comprising the administration to said subject of a rAAVO vector of the invention comprising said nucleic acid of interest.
• the invention provides a method for the delivery of a nucleic acid of interest in a cell of a subject in need thereof, comprising multiple administrations of the rAAVO vector of the invention comprising said nucleic acid of interest. Since the rAAVO vector of the invention does not induce an immune response, such a multiple administration strategy will not be impaired by the host immune system response against the rAAVO vector of the invention, contrary to what is observed with encapsidated vectors.
• Example 1 Construction of rAAVO plasmids for rAAVO vector production
• the AAV0-GFP plasmid (“pFBGR/Blas”) was constructed as follows.
• the blasticidin S gene (2784-3183 bp) along with the Orgyia pseudotsugata immediate early- 1 promoter (Op IE-1; 2401-2692 bp) (Invitrogen, Inc.) and EM7 promoter (2707-2765 bp) in pIB/V5- His/CAT plasmid (Invitrogen Inc.) was amplified by high fidelity PCR using primer sequences 5 ' - AT AAGCTT ACGCTC AGTGGAAVGAAAAC-3 ' (SEQ ID NO: 7) and 5'- ATAAGCTTGACGTGTCAGTGTCAGTCCTGCTCCT-3' (SEQ ID NO:8).
• the 865 bp PCR product was cloned into the Hind III site of the AAV2 packaging plasmid, pFBGR (Urabe et al, 2002). Restriction mapping and DNA sequencing were carried out to confirm correct plasmid construction.
• Sf9 cell lines were established for the pFBGR/Blas plasmid.
• Spodoptera frugiperda (Sf-9) cells were transfected with the pFBGR/Blas plasmid using Cellfectin (Invitrogen). Following transfections, cells were incubated for 3 days at 27 °C in insect cell culture medium (HyClone Inc.). Blasticidin S HC1 (50 ⁇ g/ml) was then added to select for stable transformants. After a two-week selection period, dilution cloning and direct colony transfer techniques were used to obtain independent clonal cell lines. Transformed cells were cultured and expanded in 10% FBS HyQ growth medium to form distinct colonies under Blasticidin S HC1 selection (10 ⁇ ).
• the Rep-Bac was as described in Urabe et al., 2002.
• the recombinant baculovirus was produced to generate sufficient quantities for animal studies as described in Virag et al., 2009. Following Rep-Bac infection, many cell lines were found to express GFP under fluorescence microscopy and also by flow cytometry (Guava EasyCyte). Extrachromosomal DNA was extracted from the Rep-Bac cells and analyzed by agarose gel electrophoresis.
• AAV0-GFP vector DNA extraction was performed with a Qiagen miniprep kit from cultured cells (1 mL) to confirm the presence of AAV0-GFP vector DNA. Larger scale DNA extraction can be carried out using a Qiagen gigaprep kit.
• Example 3 rAAVO vector-mediated gene expression in vitro
• Microinjection of rAAVO-GFP vector into nuclei or cytoplasm of 293 cells and C2C12 cells was carried out using a Xenoworks microinjection system (Sutter Instruments). Tetramethylrhodamine 70,000 MW lysine-fixable dextran was co-mi croinjected as an area marker of microinjection. Nuclei were stained with DAPI.
• plasmid-DNA needs to be delivered directly into the nucleus and cytoplasmic microinjections are not effective.
• C2C12 myoblasts were grown and differentiated for 2 days. Microinjections of a solution (0.02 mg/ml) of AAV0-GFP vector into nuclei or cytoplasm of C2C12 myotubes were carried out using a Xenoworks microinjection system (Sutter Instruments).
• Tetramethylrhodamine 70,000 MW lysine- fixable dextran was also co-mi croinjected as an area marker of microinjection. 48 hours after microinjections, myotubes were fixed using paraformaldehyde 3.7% (Sigma) and permeabilized with 0.5% triton. All fluorescent stainings were mounted in Fluoromont G (Southern Biotech). Nuclei were stained using DAPI (Sigma). Fluorescent images shown in figure 5 were acquired using a Nikon Ti microscope equipped with a CoolSNAP HQ2 camera (Roper Scientific), using a 40x 1.0 NA PL APO oil objective, driven by Metamorph (Molecular Devices). See Figure 5b.
• Fig. 5b show that cell nuclei became stained by fluorescent dye, which in turn indicates that the construct was delivered to the nucleus.
• GFP florescence confirmed GFP expression, which in turn indicates transcription from of the transduced rAAVO-GFP vector.
• Example 4 rAAVO vector-mediated gene expression in vivo via intra-arterial injection
• Intra-arterial injection of AAVO-GFP vector into the femoral artery was conducted by anesthetizing C57BL/6 mice, isolating the right hind limb for single manual, high-pressure injections, or both limbs for double manual high-pressure injections.
• a catheter was introduced into the femoral artery and 100 ⁇ g of the AAVO-GFP vector preparation in 1 ml of phosphate-buffered saline (PBS) was injected at a rate of 100 ml/s.
• PBS phosphate-buffered saline
• One minute after infusion the femoral vein was undamped ligated to open circulation. Limbs were analyzed for GFP expression 2 weeks after infusion.
• Example 5 rAAVO vector-mediated gene expression in vivo does not elicit an immune response
• mice received two high powered intra-femoral injections of AAVO-GFP in one week intervals. The first injection was performed in the left leg (100 ⁇ g of AAVO-GFP in 1 ml of PBS), and the second a week later in the right leg (100 ⁇ g of AAVO-GFP in 1 ml of PBS). Mice were allowed to recover for 8 weeks after the second injection prior to analysis under a conventional Zeiss fluorescence microscope. Normally, re-administration of rAAV after >48h is impossible due to the presence of neutralizing antibodies (Lorain et al., 2008). The fact that re-injection after 1 week results in undiminished contralateral leg transduction indicates absence of an immune response against the rAAVO vector.
• Example 6 rAAVO vector-mediated gene expression via sub-retinal injection
• rAAVO vectors will contain a tissue-specific promoter such as the cell-specific G-protein-coupled receptor kinase 1 (GRKl) promoter, which is capable of establishing robust transgene expression in rod and cone photoreceptors (Khani et al, 2007).
• GRKl cell-specific G-protein-coupled receptor kinase 1
• Another promoter example would be the ubiquitous smCBA promoter which efficiently targets the neural retina (Haire et al, 2006). These promoters can be linked as control elements to a desired transgene which is lacking expression in the disease to be treated, such as the guanylate cyclase- 1 gene, mutations of which lead to Leber Congenital Amaurosis (Boye et al, 2010) or to the RPE 65 gene, also leading to Leber Congenital Amaurosis (Lheriteau et al, 2010), or to the RD 10 gene leading to recessive retinitis pigmentosa if mutated (Pang et al, 2011).
• a desired transgene which is lacking expression in the disease to be treated, such as the guanylate cyclase- 1 gene, mutations of which lead to Leber Congenital Amaurosis (Boye et al, 2010) or to the RPE 65 gene, also leading to Leber Congenital Amaurosis (
• Example 7 rAAVO vector-mediated gene expression in vivo via systemic injection
• mice (C57BL/6) will be administered rAAVO-GFP as described in Example 2 and Figure 1 through tail- vein injections.
• AAV0-GFP preparation will consist of 100-200 ⁇ g of the rAAVO-GFP in 0.5 ml of phosphate-buffered saline (PBS).
• Tissues e.g., muscles, heart, brain, liver, kidney
• PBS phosphate-buffered saline
• Example 8 Exosome- and/or microparticle-mediated delivery of rAAVO vector
• the invention further provides for methods of treating a subject with Duchenne muscular dystrophy by (1) establishing a myoblast culture from a muscle biopsy of a subject with DMD, (2) transduce the myoblast culture with an rAAVO vector encoding the DNA of interest, (3) collect exosomes or microparticles from the culture, and (4) introducing the collected exosomes or microparticles into the subject.
• Myoblast cells cultured from a muscle biopsy of a subject with DMD are transduced with an rAAVO vector encoding a DNA of interest.
• culture supernatant is collected and first cleared at, for example, 20 minutes at 2000 g.
• the pre-cleared supernatant is then concentrated using a spin column (e.g., Amicon spin column; Millipore, Watford, UK) at 20,000 g for 70 minutes for microparticles and 100,000 g at 70 minutes for exosomes.
• the optimal duration of ultracentrifugation can be determined experimentally.
• the suspended pellet Upon washing the ultracentrifuged pellet containing the microparticles or exosomes with, for example, PBS, the suspended pellet can be used directly or subjected to additional purification steps using antibodies against proteins known to be expressed on the surface of the vesicles by, for example, FACS, MACS, immunoprecipitation, affinity chromatography, or magnetic beads coated with specific antibodies or aptamers.
• antibodies against proteins known to be expressed on the surface of the vesicles by, for example, FACS, MACS, immunoprecipitation, affinity chromatography, or magnetic beads coated with specific antibodies or aptamers.
• Purified rAAVO-containing microparticles or exosomes are then directly injected into the affected muscle tissue of the subject with DMD, or can be incubated with cultured stem cells isolated from the patient with DMD. In the latter case, the cultured stem cells that have internalized the microparticles or exosomes can be reintroduced into the affected tissue of the patient.
• microparticles or exosomes carrying rAAVO vectors will be internalized, the vectors will enter the nucleus, and express the exogenous DNA.
• the rAAV0-U7 plasmid and vector were generated in essentially the same manner as described in Example 1. Briefly, the full U7 snRNA gene (445 bp) was amplified by PCR from mouse genomic DNA using the following primers: 5 -TAACAACATAGGAGCTGTG- 3 (SEQ ID NO:9) and 5 -CAGATACGCGTTTCCTAGGA-3 ' (SEQ ID NO: 10).
• the Sm domain (AATTTGTCTAG; SEQ ID NO: 11) was changed into smOPT (AATTTTTGGAG; SEQ ID NO: 12) as described (SI), and the histone pre-mRNA pairing region was replaced by 44 bp complementary to: a) sequences across the branching point upstream of exon 23 of the dystrophin gene (BP22: 5 -AAATAGAAGTTCATTTACACTAAC-3 '; SEQ ID NO: 13) and b) sequences immediately adjacent to the exon 23 donor splice site (SD23 : 5 ' - GGCCAAACCTCGGCTTACCT-3 '; SEQ ID NO: 14).
• U7smOPT-SD23/BP22 fragment was then introduced into the pFBGR/Blas plasmid to generate rAAV0-U7-smOPT- SD23/BP22 plasmid. Further details of the U7 snRNA construct can be found in commonly owned Provisional Patent Application 61/314,830 filed March 17, 2010, incorporated by reference in its entirety. See also Goyenvalle et al, 2004.
• the invention further provides for methods of treating a subject with Duchenne muscular dystrophy by either using intra-arterial injection of rAAV0-U7 into the femoral artery as described in Example 4 or systemic delivery as described in Example 6. Lack of immune response against the rAAVO backbone also allows repeated treatments until levels of U7 in target tissues are clinically relevant as explained in Example 5. Therapeutic use will be assessed in the mdx mouse, a well-known mouse model of DMD, for which U7 tools have been developed that allow efficient dystrophin rescue by skipping exon 23 of the dystrophin pre-mRNA (Goyenvalle et al, 2004).
• Treated animals will be sacrificed at different time points after treatment and dystrophin rescue analyzed by RT-PCR (i.e., to determine skipping levels), Western blot, and immunofluorescence on tissue cryosections (as described in Goyenvalle et al, 2004) to determine protein synthesis and localization.
• RT-PCR i.e., to determine skipping levels
• Western blot Western blot
• immunofluorescence on tissue cryosections as described in Goyenvalle et al, 2004 to determine protein synthesis and localization.
• Example 11 Structural characterization of the AAV0 vector
• Electron microscopy of an rAVVO vector in the presence of SSB has also been performed to confirm the single-stranded nature of the rAAVO vector.
• AAV samples were diluted in IX TE (10 mM Tris. 1 mM EDTA. pH 8) at approximately 15 ng/ ⁇ . 30 ⁇ of the diluted samples were then incubated with 1 ⁇ of 10 mg/ml T4 Gene 32 protein (which is a SSB protein), 15 minutes a 37°C. The samples were then purified on a Superose 6 filtration column previously equilibrated in IX TE buffer to remove excess protein. The samples were then deposited on copper grids carbonated and functionalized with pentylamine.
• rAAVO appears as a linear structure, which is single stranded as revealed by SSB binding.
• rAAVo samples were separated on 4-12% SDS-PAGE (NuPAGE Tris-Acetate Mini Gels, Invitrogen) and silver stained stained (Silver Stain Plus, BioRad) for proteins.
• AAVo(GFP) encoding GFP under the CMV promoter
• AAVo(U7) harboring an expression cassette for a U7 snRNA.
• different amounts of DNA were loaded on gel:
• a capsid-free adeno-associated viral vector comprising two AAV inverted terminal repeats (ITRs) and an expression cassette, each of said ITRs having an interrupted palindromic sequence forming a hairpin structure, the cassette comprising at least one promoter operatively linked to an exogenous DNA , wherein:
• the expression cassette is flanked on each end by one inverted terminal repeat, the vector does not encode AAV capsid proteins, and the vector is not encapsidated.
• the AAV0 vector of embodiment 1, wherein the exogenous DNA comprises from about 4,200 to about 15000 nucleotides.
• a method of producing a capsid-free adeno-associated viral (AAVO) vector comprising:
• the expression cassette is flanked on each end by one inverted terminal repeat and does not encode AAV capsid proteins, and the cells do not express AAV capsid proteins;
• step (a) further comprise a selection marker.
• a method for mediating the expression of exogenous DNA in a mammalian cell comprising the steps of:
• AAVO AAV inverted terminal repeats
• ITRs AAV inverted terminal repeats
• the cassette comprising at least one promoter operatively linked to the exogenous DNA, wherein (i) the expression cassette is flanked on each end by one inverted terminal repeat, (ii) the vector does not encode AAV capsid proteins, and (iii) the vector is not encapsidated; and (iv) the vector is not immunogenic.
• a method for mediating the expression of exogenous DNA in an organ or tissue of a mammal comprising the steps of:
• a capsid-free adeno-associated viral (AAVO) vector comprising two AAV inverted terminal repeats (ITRs) and an expression cassette, each of said ITRs having an interrupted palindromic sequence forming a hairpin structure, the cassette comprising at least one promoter operatively linked to the exogenous DNA, wherein (i) the expression cassette is flanked on each end by one inverted terminal repeat, (ii) the vector does not encode AAV capsid proteins, and (iii) the vector is not encapsidated(b) waiting for cells within said organ or tissue to elaborate the expression of the exogenous DNA;
• AAVO capsid-free adeno-associated viral
• the effective amount is sufficient to permit a desired level of expression by the cells of the exogenous DNA.
• systemic delivery comprises intra-arterial or intramuscular injection.
• delivering step comprises sub-retinal injection.
• AAVO vector comprises a promoter directing the expression of said exogenous DNA preferentially or exclusively in a specific organ or tissue.
• a method for the treatment of a disease in a subject in need thereof, the disease involving a genetic defect manifesting symptoms due to reduced or ceased expression of a polypeptide or in expression of a nonfunctional or poorly functional analog of said polypeptide comprising delivering to said subject an effective amount of a vector according to embodiment 1, wherein the exogenous DNA comprises an oligonucleotide or polynucleotide that skips, corrects, silences or masks the defect, resulting in amelioration of symptoms associated with the disease or disorder.
• a method according to embodiment 32 comprising delivering to said subject an effective amount of a vector according to embodiment 1, wherein the exogenous DNA encodes RNAi, or siRNA or an antisense oligonucleotide or polynucleotide.
• a method according to embodiment 32 comprising delivering to said subject an effective amount of a vector according to embodiment 1, wherein the exogenous DNA encodes an oligo or polynucleotide the expression of which would result in amelioration of symptoms associated with the disease by restoring at least partial function of said polypeptide.
• a method for effecting the expression of a desired gene product or oligonucleotide in a cell comprising contacting at least one rAAVO vector with the cell's surface in the absence of a transfection agent or additional physical means to facilitate entry of said rAAVO vector into the cell.
• rAAV adeno-associated viral vectors as therapeutic tools for Duchenne muscular dystrophy
• LARGE can functionally bypass alpha-dystroglycan glycosylation defects in distinct congenital muscular dystrophies. Nat Med. 2004 Jul;10(7):696-703.
• AAV plasmid DNA simplifies liver-directed in vivo gene therapy: comparison of expression levels after plasmid DNA-, adeno-associated virus- and adenovirus-mediated liver transfection. J Gene Med. 2010 Oct;12(10):810-7. Dong JY, Fan PD, Frizzell RA. Quantitative analysis of the packaging capacity of recombinant adeno-associated virus. Hum Gene Ther. 1996;7(17):2102-12.
• Intravascular AAV9 preferentially targets neonatal neurons and adult astrocytes. Nat Biotechnol. 2009 Jan;27(l):59-65.
• McCarty DM Self-complementary AAV vectors; advances and applications. Mol Ther. 2008 Oct; 16(10): 1648- 56. Epub 2008 Aug 5. Millington-Ward S, Chadderton N, O'Reilly M, Palfi A, Goldmann T, Kilty C, Humphries M, Wolfram U, Bennett J, Humphries P, Kenna PF, Farrar G. Suppression and Replacement Gene Therapy for Autosomal Dominant Disease in a Murine Model of Dominant Retinitis Pigmentosa. Mol Ther. 2011 Jan 11
• Stieger K Chauveau C, Rolling F. Preclinical studies on specific gene therapy for recessive retinal degenerative diseases. Curr Gene Ther. 2010 Oct l;10(5):389-403. Stieger K, Lorenz B. Gene therapy for vision loss ⁇ recent developments. Discov Med. 2010 Nov;10(54):425- 33. Sun N, Liang J, Abil Z, Zhao H. Optimized TAL effector nucleases (TALENs) for use in treatment of sickle cell disease. Mol Biosyst. 2012 Apr 1;8(4): 1255-63.
• TALENs Optimized TAL effector nucleases
• Toromanoff A Adjali O, Larcher T, Hill M, Guigand L, Chenuaud P, Deschamps JY, Gauthier O, Blancho G, Vanhove B, Rolling F, Cherel Y, Moullier P, Anegon I, Le Guiner C. Lack of immunotoxicity after regional intravenous (RI) delivery of rAAV to nonhuman primate skeletal muscle. Mol Ther. 2010 Jan; 18(1): 151-60.
• Varenika V Kells AP, Valles F, Hadaczek P, Forsayeth J, Bankiewicz KS. Controlled dissemination of AAV vectors in the primate brain. Prog Brain Res. 2009;175: 163-72.
• Adeno-associated virus AAV based gene therapy for eye diseases. Cell Tissue Bank. 2011 Feb 23. Epub ahead of print.
• Recombinant adeno-associated virus serotype 4 mediates unique and exclusive long-term transduction of retinal pigmented epithelium in rat, dog, and nonhuman primate after subretinal delivery. Mol Ther. 2003 Jun;7(6):774-81.

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